Interaction of B-DNA and Monovalent Cations: Theory and Practice in X-Ray Crystallography

Abstract

In this thesis, fundamental questions about the nature of the solvent/counter-ion region of x-ray crystal structures are raised. The ambiguity in the identity and occupancy of the molecular and atomic species in this region is explored experimentally. Anomalous scattering is proposed as a possible method for resolving this ambiguity. To this effect, the properties of rubidium I and thallium I are compared and contrasted to each other and to other group I metals.

Finally, the structures of two modified B-DNA dodecamers are determined to explore the effect of monovalent cations on B-DNA structure. The modifications in these structures harbor tethered cations that are covalently linked to the DNA in the major groove. In one structure, the tethered cation causes axial bending of the DNA molecule, while in the second structure the molecule remains linear. We posit that the discrepancy between the two structures is due to lattice packing forces. In addition, we show evidence for the displacement of thallium I cations from the major groove of the bent structure.